From 173905b38b5d586f53ca2b9d358acf5088bea84c Mon Sep 17 00:00:00 2001 From: Brian McMahon Date: Tue, 20 Feb 2024 12:16:59 +0000 Subject: [PATCH 1/4] Dictionary file Topology.dic amended to accommodate proof corrections to Chapters 3.9 and 4.9 of International Tables G 2nd edition; some minor style changes to text of definitions; examples imported from external file topo_examples.cif. --- Topology.dic | 18 +- topo_examples.cif | 536 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 552 insertions(+), 2 deletions(-) create mode 100644 topo_examples.cif diff --git a/Topology.dic b/Topology.dic index 1275723..b96b367 100644 --- a/Topology.dic +++ b/Topology.dic @@ -9,8 +9,8 @@ data_TOPOLOGY_CIF _dictionary.title TOPOLOGY_CIF _dictionary.class Instance - _dictionary.version 0.9.6 - _dictionary.date 2024-02-13 + _dictionary.version 0.9.7 + _dictionary.date 2024-02-20 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/TopoCif/master/Topology.dic _dictionary.ddl_conformance 4.1.0 @@ -2038,4 +2038,18 @@ save_ Changed the _type.source attribute of all SU data items to 'Related'. (A. Vaitkus) +; + 0.9.7 2024-02-20 +; + Removed _topol_link.net_id and _topol_net.overall_topology in line + with proof corrections of draft chapters 3.9 and 4.9 by Blatov et al. + (B. McMahon) + + Replaced example placeholders in TOPOL category by _import.get of + associated topo_examples.cif file. + (B. McMahon) + + Made various small style and punctuation changes to prepare for + publication in International Tables Volume G. + (B. McMahon) ; diff --git a/topo_examples.cif b/topo_examples.cif new file mode 100644 index 0000000..1420786 --- /dev/null +++ b/topo_examples.cif @@ -0,0 +1,536 @@ +save_topol_examples + +loop_ + _description_example.case + _description_example.detail + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 1/4-x,1/4-y,z + # - - - - data truncated for brevity - - - - + 13 -y,-x,-z + # - - - - data truncated for brevity - - - - + 192 3/4-z,1/2+y,1/4-x + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + C1 0.12500 0.12500 0.12500 + +loop_ + _topol_net.id + _topol_net.overall_topology_RCSR + 1 dia + +loop_ + _topol_node.id + _topol_node.net_id + 1 1 + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.symop_id_1 + _topol_link.translation_1 + _topol_link.symop_id_2 + _topol_link.translation_2 + _topol_link.distance + _topol_link.Voronoi_solid_angle + _topol_link.type + _topol_link.order + _topol_link.multiplicity + 1 1 1 1 [0 0 0] 13 [0 0 0] 1.5446 22.04 v 1 16 + +loop_ + _topol_atom.id + _topol_atom.node_id + _topol_atom.atom_label + _topol_atom.element_symbol + 1 1 C1 C +; + +; +Example 1 - Connectivity of the diamond crystal structure. + All atoms coincide with the nodes and all bonds coincide + with the edges, so the atomic network coincides with the + underlying net. +; + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 -x,-y,z + 3 x,-y,-z + # - - - - data truncated for brevity - - - - + 24 -z,y,-x + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + Li1 0.00000 0.00000 0.00000 + C1 0.31850 0.31850 0.31850 + O1 0.19920 0.19920 0.19920 + Co1 0.50000 0.50000 0.50000 + +loop_ + _topol_net.id + _topol_net.label + _topol_net.z_number + _topol_net.special_details + _topol_net.overall_topology_TOPOS + 1 Net_1 2 'Atomic network' 'Unknown' + 2 Net_2 2 'Underlying net with carbonyl ligands as nodes' '2,4T3' + +loop_ + _topol_node.id + _topol_node.label + _topol_node.net_id + _topol_node.fract_x + _topol_node.fract_y + _topol_node.fract_z + 1 Li1 1 . . . # Li + 2 C1 1 . . . # C + 3 O1 1 . . . # O + 4 Co1 1 . . . # Co + 5 ZA1 2 . . . # Li + 6 ZB1 2 0.25036 0.25036 0.25036 # (CO) + 7 ZC1 2 . . . # Co + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.distance + _topol_link.type + 1 1 3 1.9121 v # Li1-O1 + 2 2 3 1.1452 v # C1-O1 + 3 2 4 1.7422 v # C1-Co1 + 4 5 6 2.4032 gl # Li1-(CO) + 5 6 7 2.3963 gl # (CO)-Co + +loop_ + _topol_atom.id + _topol_atom.node_id + _topol_atom.atom_label + _topol_atom.element_symbol + 1 1 Li1 Li + 2 2 C1 C + 3 3 O1 O + 4 4 Co1 Co + 5 5 Li1 Li + 6 6 C1 C + 7 6 O1 O + 8 7 Co1 Co +; + +; Example 2 - Connectivity of atomic and underlying nets for an + interpenetrating array of two LiCo(CO)4 networks. The atomic net + consists of Li, C, O, and Co atoms, while the underlying net is built + from three kinds of nodes: Li and Co atoms and carbonyl (CO) ligand; + the nodes are labeled as ZA1, ZC1, and ZB1, respectively. Two + possible variants are shown: the coordinates of ZA1 are specified by + a reference to the Li1 atom, while the coordinates of ZC1 are specified + explicitly. Both atomic and underlying nets are described in the + TOPOL_NET section. +; + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 -y,x-y,z + 3 -x+y,-x,z + # - - - - data truncated for brevity - - - - + 20 1/3+x-y,2/3-y,1/6-z + # - - - - data truncated for brevity - - - - + 36 1/3-y,2/3-x,1/6+z + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + C1 0.00000 0.00000 0.25000 + O1 0.25930 0.00000 0.25000 + Ca1 0.00000 0.00000 0.00000 + +loop_ + _topol_net.id + _topol_net.overall_topology_RCSR + 1 pcu-b + +loop_ + _topol_node.id + _topol_node.label + 1 ZA1 # CO3 + 2 ZB1 # Ca + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.symop_id_2 + _topol_link.translation_2 + _topol_link.distance + _topol_link.type + 1 1 2 20 [-1 -1 0] 3.2122 gl # (CO3)-Ca + +loop_ + _topol_atom.id + _topol_atom.node_id + _topol_atom.atom_label + _topol_atom.element_symbol + _topol_atom.symop_id + 1 1 C1 C 1 + 2 1 O1 O 1 + 3 1 O1 O 2 + 4 1 O1 O 3 + 5 2 Ca1 Ca 1 +; + +; Example 3 - Connectivity of an underlying net of the calcite + (CaCO3) crystal structure. The nodes of the underlying + net correspond to Ca atoms and carbonate (CO3) groups. +; + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 1/2-x,1/2-y,z + # - - - - data truncated for brevity - - - - + 13 -y,-x,-z + # - - - - data truncated for brevity - - - - + 48 1/2-z,y,1/2-x + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + O1 0.25000 0.25000 0.25000 + Cu1 0.00000 0.00000 0.00000 + +loop_ + _topol_net.id + _topol_net.z_number + _topol_net.overall_topology_RCSR + 1 2 'dia' + +loop_ + _topol_node.id + _topol_node.net_id + 1 1 + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.symop_id_2 + _topol_link.type + 1 1 1 13 gl + +loop_ + _topol_atom.id + _topol_atom.node_id + _topol_atom.link_id + _topol_atom.atom_label + _topol_atom.element_symbol + 1 1 . O1 O + 2 . 1 Cu1 Cu +; + +; Example 4 - Connectivity of an underlying net of the cuprite (Cu2O) + crystal structure. Oxygen atoms coincide with the nodes, + while copper atoms represent the edges. There are two + interpenetrating networks of the diamond topology. +; +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + # - - - - data truncated for brevity - - - - + 5 z,x,y + # - - - - data truncated for brevity - - - - + 26 x,y,-z + # - - - - data truncated for brevity - - - - + 37 y,x,z + # - - - - data truncated for brevity - - - - + 192 1/2-z,1/2+y,-x + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + H1 0.30590 0.19410 0.04520 + C1 0.25000 0.25000 0.11050 + C2 0.28310 0.21690 0.02630 + C3 0.25000 0.25000 0.05380 + O1 .25000 0.25000 0.25000 + O2 0.28180 0.21820 0.13390 + Zn1 0.29350 0.20650 0.20650 + +loop_ + _topol_net.id + _topol_net.label + _topol_net.special_details + _topol_net.overall_topology_TOPOS + 1 Net_1 'Atomic network' 'Unknown' + 2 Net_2 'Underlying net with zinc tetranuclear complex groups as nodes and benzene rings as links (cluster representation)' 'pcu' + 3 Net_3 'Underlying net with zinc, oxygen and benzenedicarboxylato ligands as 4-coordinate nodes (standard representation)' 'fff' + +loop_ + _topol_node.id + _topol_node.net_id + 1 1 # H1 + 2 1 # C1 + 3 1 # C2 + 4 1 # C3 + 5 1 # O1 + 6 1 # O2 + 7 1 # Zn1 + 8 2 # C6O13Zn4 + 9 3 # C8H4O4 + 10 3 # O1 + 11 3 # Zn1 + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.symop_id_2 + _topol_link.distance + _topol_link.type + 1 1 3 . 0.9594 v # H1-C2 + 2 2 6 37 1.3013 v # C1-O2 + 3 2 4 . 1.4554 ar # C1-C3 + 4 3 3 26 1.3502 ar # C2-C2 + 5 3 4 . 1.3936 ar # C2-C3 + 6 5 7 . 1.9340 v # O1-Zn1 + 7 6 7 . 1.9114 v # O2-Zn1 + 8 8 8 26 12.8345 gl # (C6O13Zn4)-(C6H4)-(C6O13Zn4) + 9 9 11 5 5.5309 gl # (C8H4O4)-Zn1 + 10 10 11 . 1.9341 v # O1-Zn1 + +loop_ + _topol_atom.id + _topol_atom.atom_label + _topol_atom.node_id + _topol_atom.link_id + _topol_atom.symop_id + _topol_atom.element_symbol + 1 H1 1 . 1 H + 2 C1 2 . 1 C + 3 C2 3 . 1 C + 4 C3 4 . 1 C + 5 O1 5 . 1 O + 6 O2 6 . 1 O + 7 Zn1 7 . 1 Zn + 10 C1 8 . 1 C + 11 C1 8 . 55 C + 12 O2 8 . 55 O + 13 O2 8 . 80 O + 14 O2 8 . 6 O + 15 O2 8 . 59 O + 16 O2 8 . 42 O + 17 O2 8 . 78 O + 18 C1 8 . 78 C + 19 C1 8 . 5 C + 20 Zn1 8 . 6 Zn + 21 Zn1 8 . 55 Zn + 22 C1 8 . 69 C + 23 C1 8 . 6 C + 24 O2 8 . 41 O + 25 O2 8 . 69 O + 26 O1 8 . 1 O + 27 O2 8 . 5 O + 28 O2 8 . 82 O + 29 Zn1 8 . 5 Zn + 30 Zn1 8 . 1 Zn + 31 O2 8 . 1 O + 32 O2 8 . 37 O + 33 O2 9 . 14 O + 34 O2 9 . 26 O + 35 O2 9 . 1 O + 36 O2 9 . 37 O + 37 C1 9 . 14 C + 38 C3 9 8 14 C + 39 C2 9 8 14 C + 40 H1 9 8 14 H + 41 C2 9 8 37 C + 42 H1 9 8 37 H + 43 C2 9 8 26 C + 44 H1 9 8 26 H + 45 C2 9 8 1 C + 46 H1 9 8 1 H + 47 C3 9 8 1 C + 48 C1 9 . 1 C + 49 O1 10 . 1 O + 50 Zn1 11 . 1 Zn +; +# +; Example 5 - MOF-5 (multiple nets; two polyatomic nodes and a molecular + linker). +; + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 1/2-x,-y,1/2+z + 3 1/2+x,1/2-y,-z + 4 -x,1/2+y,1/2-z + 5 -x,-y,-z + 6 1/2+x,y,1/2-z + 7 1/2-x,1/2+y,z + 8 x,1/2-y,1/2+z + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + H1 0.19700 0.11100 0.02200 + H2 0.05900 0.26600 0.08700 + C1 0.14120 0.08370 0.23120 + N1 0.14590 0.16990 0.10179 + N2 0.14010 0.01250 0.34609 + +loop_ + _topol_node.id + 1 2 3 4 5 + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.distance + _topol_link.symop_id_2 + _topol_link.translation_2_x + _topol_link.translation_2_y + _topol_link.translation_2_z + _topol_link.type + _topol_link.order + 1 1 4 0.8988 1 0 0 0 v 1 # H1-N1 + 2 1 5 2.1228 2 0 0 -1 hb ? # H1-N2 + 3 2 4 0.8826 1 0 0 0 v 1 # H2-N1 + 4 2 5 2.2152 4 0 0 0 hb ? # H2-N2 + 5 3 5 1.1520 1 0 0 0 v 3 # C1-N2 + 6 3 4 1.3148 1 0 0 0 v 1 # C1-N1 + +loop_ + _topol_atom.id + _topol_atom.atom_label + _topol_atom.node_id + _topol_atom.element_symbol + 1 H1 1 H + 2 H2 2 H + 3 C1 3 C + 4 N1 4 N + 5 N2 5 N +; + +; Example 6 - Cyanamide (simple atomic network example with hydrogen bonding). +; + +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +; +loop_ + _space_group_symop.id + _space_group_symop.operation_xyz + 1 x,y,z + 2 1/4-x,1/4-y,z + # - - - - data truncated for brevity - - - - + 13 -y,-x,-z + # - - - - data truncated for brevity - - - - + 41 x,z,y + 42 z,y,x + # - - - - data truncated for brevity - - - - + 47 x,1/4-z,1/4-y + # - - - - data truncated for brevity - - - - + 192 3/4-z,1/2+y,1/4-x + +loop_ + _atom_site.label + _atom_site.fract_x + _atom_site.fract_y + _atom_site.fract_z + Si1 0.94690 0.12510 0.03640 + +loop_ + _topol_net.id + _topol_net.overall_topology_IZA + 1 FAU + +loop_ + _topol_node.id + _topol_node.net_id + _topol_node.label + 1 1 Si + +loop_ + _topol_link.id + _topol_link.node_id_1 + _topol_link.node_id_2 + _topol_link.distance + _topol_link.symop_id_2 + _topol_link.translation_2 + _topol_link.type + 1 1 1 3.0470 47 [0 0 0] gl + 2 1 1 3.0473 13 [1 1 0] gl + 3 1 1 3.0539 41 [0 0 0] gl + 4 1 1 3.0814 42 [1 0 -1] gl + +loop_ + _topol_atom.id + _topol_atom.node_id + _topol_atom.atom_label + _topol_atom.element_symbol + 1 1 Si1 Si + +loop_ + _topol_tiling.id + _topol_tiling.net_id + _topol_tiling.signature + _topol_tiling.vertices + _topol_tiling.edges + _topol_tiling.faces + _topol_tiling.tiles + _topol_tiling.d_size + 1 1 '2[4^6.6^2]+[4^6.6^8]+[4^18.6^4.12^4]' 1 4 5 3 24 +; + +; Example 7 - FAU zeolite tiling example. +; +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +save_ + + From 7286e0a14de174c9e78902cc4359aab7543d7084 Mon Sep 17 00:00:00 2001 From: Brian McMahon Date: Tue, 20 Feb 2024 12:34:27 +0000 Subject: [PATCH 2/4] Dictionary file Topology.dic amended to accommodate proof corrections to Chapters 3.9 and 4.9 of International Tables G 2nd edition; some minor style changes to text of definitions; examples imported from external file topo_examples.cif. --- Topology.dic | 167 +++++++++++++++------------------------------------ 1 file changed, 48 insertions(+), 119 deletions(-) diff --git a/Topology.dic b/Topology.dic index b96b367..3e5e1ab 100644 --- a/Topology.dic +++ b/Topology.dic @@ -54,51 +54,8 @@ save_TOPOL _name.category_id TOPOLOGY _name.object_id TOPOL - loop_ - _description_example.case - _description_example.detail -; - [ex 1] -; -; - Example 1 -; -; - [ex 2] -; -; - Example 2 -; -; - [ex 3] -; -; - Example 3 -; -; - [ex 4] -; -; - Example 4 -; -; - [ex 5] -; -; - Example 5 -; -; - [ex 6] -; -; - Example 6 -; -; - [ex 7] -; -; - Example 7 -; + _import.get + [{'file':topo_examples.cif 'save':topol_examples}] save_ @@ -169,7 +126,7 @@ save_topol_atom.element_symbol a single element symbol found on the official IUPAC Periodic Table. For example: 'C', 'H', or 'Co', without isotope or charge. Data items in the ATOM_SITE category that do not correspond to elements - of the periodic table should be represented here as '.'. + of the Periodic Table should be represented here as '.'. ; _name.category_id topol_atom _name.object_id element_symbol @@ -288,9 +245,9 @@ save_topol_atom.translation and the original position is (0.2,0.7,1.0) in fractional coordinates, then the resultant position is (-0.3,0.2,1.0). Alternatively, _topol_atom.translation_x, - _topol_atom.translation_y, and + _topol_atom.translation_y and _topol_atom.translation_z data items may be used to - describe separate components of the vector for CIF1 compatibility. + describe separate components of the vector for CIF 1 compatibility. If this item is omitted or assigned to '.' it is assumed to be equal to [0,0,0]. ; @@ -398,7 +355,7 @@ save_TOPOL_LINK _description.text ; The TOPOL_LINK category describes the crystal structure - connectivity and encodes the weighted colored + connectivity and encodes the weighted coloured symmetry-labeled quotient graph, from which the whole periodic net describing the overall topology of the crystal structure can be restored. The definition of @@ -408,8 +365,7 @@ save_TOPOL_LINK connections described in TOPOL_LINK may correspond to any vectors in the structure, not just bonds or contacts. The two end-point references are to nodes listed in TOPOL_NODE using - _topol_link.node_id_1 and _topol_link.node_id_2. - In the case of multiple nets, _topol_link.net_id is required. Other + _topol_link.node_id_1 and _topol_link.node_id_2. Other items in this category are optional. If the link itself represents atoms (as in the case of a molecular linker), the atoms comprising the link must be referenced by _topol_atom.link_id. @@ -519,26 +475,6 @@ save_topol_link.multiplicity save_ -save_topol_link.net_id - - _definition.id '_topol_link.net_id' - _definition.update 2021-10-08 - _description.text -; - The identifier of the net, to which this node belongs. -; - _name.category_id topol_link - _name.object_id net_id - _name.linked_item_id '_topol_net.id' - _type.purpose Link - _type.source Related - _type.container Single - _type.contents Integer - _enumeration.range 1: - _units.code none - -save_ - save_topol_link.node_id_1 _definition.id '_topol_link.node_id_1' @@ -688,7 +624,7 @@ save_topol_link.translation_1 and the original position is (0.2,0.7,1.0) in fractional coordinates, then the resultant position is (-0.3,0.2,1.0). Alternatively, _topol_link.translation_1_x, - _topol_link.translation_1_y, and + _topol_link.translation_1_y and _topol_link.translation_1_z data items may be used to describe separate components of the vector. ; @@ -785,7 +721,7 @@ save_topol_link.translation_2 and the original position is (0.2,0.7,1.0) in fractional coordinates, then the resultant position is (-0.3,0.2,1.0). Alternatively, _topol_link.translation_2_x, - _topol_link.translation_2_y, and + _topol_link.translation_2_y and _topol_link.translation_2_z data items may be used to describe separate components of the vector. ; @@ -954,6 +890,7 @@ save_TOPOL_NET Reference: Delgado-Friedrichs, O., Foster, M. D., O'Keeffe, M., Proserpio, D. M., Treacy, M. M. J. & Yaghi, O. M. (2005). + What do we know about three-periodic nets? J. Solid State Chem. 178, 2533-2554, DOI:10.1016/j.jssc.2005.06.037. ; @@ -977,7 +914,8 @@ save_topol_net.genus repeat unit and the edges are all the edges of the repeat unit. Reference: Delgado-Friedrichs, O. & O'Keeffe, M. - (2005). J. Solid State Chem. 178, 2480-2485, + (2005). Crystal nets as graphs: Terminology and definitions. + J. Solid State Chem. 178, 2480-2485, DOI:10.1016/j.jssc.2005.06.011. ; _name.category_id topol_net @@ -1027,24 +965,6 @@ save_topol_net.label save_ -save_topol_net.overall_topology - - _definition.id '_topol_net.overall_topology' - _definition.update 2018-01-30 - _description.text -; - The overall topology symbol in an arbitrary form. -; - _name.category_id topol_net - _name.object_id overall_topology - _type.purpose Describe - _type.source Assigned - _type.container Single - _type.contents Text - _description_example.case 'face-centered cubic topology' - -save_ - save_topol_net.overall_topology_epinet _definition.id '_topol_net.overall_topology_EPINET' @@ -1070,7 +990,7 @@ save_topol_net.overall_topology_iza _definition.update 2018-01-30 _description.text ; - The three-letters symbol for a Zeolite Framework Types that has + The three-letter symbol for a Zeolite Framework Types that has been approved by the Structure Commission of the International Zeolite Association (IZA-SC). @@ -1097,7 +1017,9 @@ save_topol_net.overall_topology_rcsr by O'Keeffe et al. (2008). Reference: O'Keeffe, M., Peskov, M. A., Ramsden, S. J. & Yaghi, O. M. - (2008). Acc. Chem. Res. 41, 1782-1789, DOI:10.1021/ar800124u. + (2008). The Reticular Chemistry Structure Resource (RCSR) Database of, + and Symbols for, Crystal Nets. Acc. Chem. Res. 41, 1782-1789, + DOI:10.1021/ar800124u. ; _name.category_id topol_net _name.object_id overall_topology_RCSR @@ -1118,8 +1040,9 @@ save_topol_net.overall_topology_sp The overall topology symbol according to the nomenclature of Fischer for sphere packings described by Koch et al. (2006). - Reference: Koch, E., Fischer, W. & Sowa, H. (2006). Acta Cryst. - A62, 152-167, DOI:10.1107/S010876730600362X. + Reference: Koch, E., Fischer, W. & Sowa, H. (2006). Interpenetration + of homogeneous sphere packings and of two-periodic layers of spheres. + Acta Cryst. A62, 152-167, DOI:10.1107/S010876730600362X. ; _name.category_id topol_net _name.object_id overall_topology_SP @@ -1142,12 +1065,13 @@ save_topol_net.overall_topology_topos (coordination numbers) of all independent nodes; D is one of the letters C (chain), L (layer) or T (three-periodic) designating the dimensionality of the net; and n enumerates non-isomorphic nets with a given ND sequence. - For finite (molecular) graphs the symbols NMK-n are used, where k is the + For finite (molecular) graphs the symbols NMk-n are used, where k is the number of vertices (atoms) in the graph. Reference: Aman, F., Asiri, A. M., Siddiqui, W. A., Arshad, M. N., - Ashraf, A., Zakharov, N. S. & Blatov, V. A. (2014). Cryst. Eng. Comm, - 16, 1963-1970, DOI:10.1039/C3CE42218F. + Ashraf, A., Zakharov, N. S. & Blatov, V. A. (2014). Multilevel + topological description of molecular packings in 1,2-benzothiazines. + Cryst. Eng. Comm, 16, 1963-1970, DOI:10.1039/C3CE42218F. ; _name.category_id topol_net _name.object_id overall_topology_TOPOS @@ -1281,11 +1205,9 @@ save_TOPOL_NODE _description.text ; The TOPOL_NODE category, along with TOPOL_ATOM, describes the topological - properties, position, and chemical composition - of the nodes of the underlying net. The TOPOL_NODE category is optional. - It is only required for polyatomic nodes or in cases where the - label given to the node is different from _atom_site.label. Data items - _topol_node.fract_x, _topol_node.fract_y, and _topol_node.fract_z must be + properties, position and chemical composition + of the nodes of the underlying net. Data items + _topol_node.fract_x, _topol_node.fract_y and _topol_node.fract_z must be present only if the node's position cannot be derived from other data items in TOPOL_NODE or TOPOL_ATOM. Fractional coordinates can be given in other @@ -1294,6 +1216,8 @@ save_TOPOL_NODE In the case of multiple nets, _topol_node.net_id is also required. Reference: Blatov, V. A., O'Keeffe, M. & Proserpio, D. M. (2010). + Vertex-, face-, point-, Schl\"afli-, and Delaney-symbols in nets, + polyhedra and tilings: recommended terminology. Cryst. Eng. Comm. 12, 44-48, DOI:10.1039/B910671E. ; _name.category_id TOPOLOGY @@ -1335,7 +1259,7 @@ save_topol_node.coordination_sequence_plain _definition.update 2021-07-28 _description.text ; - A CIF1-compatible alternative representation of the coordination sequence + A CIF 1 compatible alternative representation of the coordination sequence as plain text, as a quoted string of white-space-separated numbers. ; _name.category_id topol_node @@ -1355,7 +1279,7 @@ save_topol_node.extended_point_symbol _definition.update 2021-10-20 _description.text ; - The extended point symbol of a N-coordinated node lists all shortest + The extended point symbol of an N-coordinated node lists all shortest circuits for each of the N(N-1)/2 angles (pairs of edges) incident to the node. It is written as A(a).B(b)... where A, B, ... designate sizes of circuits, which meet at angles A, B, ..., and a, b, ... designate numbers @@ -1375,13 +1299,13 @@ save_topol_node.extended_point_symbol _description_example.case _description_example.detail 6(2).6(2).6(2).6(2).6(2).6(2) - 'ES for a vertex in the diamond structure' + 'extended symbol for a vertex in the diamond structure' 4.6(2).4.8(3).6(2).6(2) - 'ES for one vertex of feldspar net' + 'extended symbol for one vertex of feldspar net' 7(2).9(2).7(3).7(3).7(3).7(3) - 'ES for the vertex of qzd net' + 'extended symbol for the vertex of qzd net' 4.4.4.4.6(3).6(3).6(5).6(5).6(5).6(5) - 'ES for the vertex of 5-c sqp net' + 'extended symbol for the vertex of 5-c sqp net' save_ @@ -1639,10 +1563,13 @@ save_topol_node.vertex_symbol loop_ _description_example.case _description_example.detail - 6(2).6(2).6(2).6(2).6(2).6(2) 'Vertex symbol for diamond' - 4.6(2).4.8.6.6(2) 'VS for one vertex of feldspar net' - 7(2).*.7(3).7(3).7(3).7(3) 'VS for the vertex of qzd net' - 4.4.4.4.6.6.6(5).6(5).6(5).6(5) 'VS for the vertex of 5-c sqp net' + 6(2).6(2).6(2).6(2).6(2).6(2) 'vertex symbol for diamond' + 4.6(2).4.8.6.6(2) + 'vertex symbol for one vertex of feldspar net' + 7(2).*.7(3).7(3).7(3).7(3) + 'vertex symbol for the vertex of qzd net' + 4.4.4.4.6.6.6(5).6(5).6(5).6(5) + 'vertex symbol for the vertex of 5-c sqp net' save_ @@ -1662,8 +1589,7 @@ save_topol_node.wyckoff_symbol _type.container Single _type.contents Text - _import.get - [{'file':templ_enum.cif 'save':Wyckoff_letter}] + _import.get [{'file':templ_enum.cif 'save':Wyckoff_letter}] save_ @@ -1677,7 +1603,7 @@ save_TOPOL_TILING ; The TOPOL_TILING category describes the natural tiling corresponding to the underlying net. A tiling is a - partition of crystal space using generalised polyhedra, and a + partition of crystal space using generalized polyhedra, and a natural tiling is one for which tiles are the smallest possible that conserve the full symmetry of the net and for which the faces are all locally strong rings. This means that there is no @@ -1688,7 +1614,8 @@ save_TOPOL_TILING the number of faces of a given size in the tile. Reference: Blatov, V. A., Delgado-Friedrichs, O., O'Keeffe M. & - Proserpio D. M. (2007). Acta Cryst. A63, 418-425, + Proserpio D. M. (2007). Three-periodic nets and tilings: natural + tilings for nets. Acta Cryst. A63, 418-425, DOI:10.1107/S0108767307038287. ; _name.category_id TOPOLOGY @@ -1704,10 +1631,12 @@ save_topol_tiling.d_size _description.text ; The number of distinct (not symmetry-related) chambers in the - tiling as expressed by the Delaney Dress symbol or just D-symbol, + tiling as expressed by the Delaney-Dress symbol or just D-symbol, as a measure of the complexity of the tiling (D-size). Reference: Blatov, V. A., O'Keeffe, M. & Proserpio, D. M. (2010). + Vertex-, face-, point-, Schl\"afli-, and Delaney-symbols in nets, + polyhedra and tilings: recommended terminology. Cryst. Eng. Comm. 12, 44-48, DOI:10.1039/B910671E. ; _name.category_id topol_tiling From c3c1d1feaacb22ef6be46d35bd157989d278b85b Mon Sep 17 00:00:00 2001 From: nautolycus <98825550+nautolycus@users.noreply.github.com> Date: Wed, 21 Feb 2024 10:41:26 +0000 Subject: [PATCH 3/4] Apply suggestions from code review Thanks for these style fixes - Brian Co-authored-by: Antanas Vaitkus --- Topology.dic | 8 +++++--- topo_examples.cif | 4 ++++ 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/Topology.dic b/Topology.dic index 3e5e1ab..5c55206 100644 --- a/Topology.dic +++ b/Topology.dic @@ -890,7 +890,7 @@ save_TOPOL_NET Reference: Delgado-Friedrichs, O., Foster, M. D., O'Keeffe, M., Proserpio, D. M., Treacy, M. M. J. & Yaghi, O. M. (2005). - What do we know about three-periodic nets? + What do we know about three-periodic nets? J. Solid State Chem. 178, 2533-2554, DOI:10.1016/j.jssc.2005.06.037. ; @@ -1563,7 +1563,8 @@ save_topol_node.vertex_symbol loop_ _description_example.case _description_example.detail - 6(2).6(2).6(2).6(2).6(2).6(2) 'vertex symbol for diamond' + 6(2).6(2).6(2).6(2).6(2).6(2) + 'vertex symbol for diamond' 4.6(2).4.8.6.6(2) 'vertex symbol for one vertex of feldspar net' 7(2).*.7(3).7(3).7(3).7(3) @@ -1589,7 +1590,8 @@ save_topol_node.wyckoff_symbol _type.container Single _type.contents Text - _import.get [{'file':templ_enum.cif 'save':Wyckoff_letter}] + _import.get + [{'file':templ_enum.cif 'save':Wyckoff_letter}] save_ diff --git a/topo_examples.cif b/topo_examples.cif index 1420786..f871c03 100644 --- a/topo_examples.cif +++ b/topo_examples.cif @@ -1,3 +1,7 @@ +#\#CIF_2.0 + +data_TOPOLOGY_EXAMPLES + save_topol_examples loop_ From c869af1b4e762ceeb2dbdde8d24c0790d0c4f84f Mon Sep 17 00:00:00 2001 From: nautolycus <98825550+nautolycus@users.noreply.github.com> Date: Wed, 21 Feb 2024 11:04:05 +0000 Subject: [PATCH 4/4] Update Topology.dic Agreed that this distinguishes this version cleanly from the version published on the IUCr website. Co-authored-by: Antanas Vaitkus --- Topology.dic | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Topology.dic b/Topology.dic index 5c55206..46d40fc 100644 --- a/Topology.dic +++ b/Topology.dic @@ -1966,12 +1966,12 @@ save_ _topol_link.symop_id_1 and _topol_link.symop_id_2 data items to be compatible with the data items that they are linked to. (A. Vaitkus) - - Changed the _type.source attribute of all SU data items to 'Related'. - (A. Vaitkus) ; 0.9.7 2024-02-20 ; + Changed the _type.source attribute of all SU data items to 'Related'. + (A. Vaitkus) + Removed _topol_link.net_id and _topol_net.overall_topology in line with proof corrections of draft chapters 3.9 and 4.9 by Blatov et al. (B. McMahon)